Kinetic Compatibility as a Predictor of PTP1B Inhibitor Combination Outcomes: An Integrated Experimental and Computational Study

Abstract

Abstract

Although chlorogenic acid, suramin, ursolic acid, and the glycyrrhetinic acid derivative FC122 are individually known PTP1B inhibitors, no study has systematically characterized how mechanistic diversity determines the pharmacological outcome of their combinations. Here, we integrate experimental enzyme kinetics, molecular docking, molecular dynamics (MD), and membrane permeability simulations to address this question. Individual inhibitory potencies ranked SUR > FC122 > UA > CGA (IC 50 : 1.82, 3.27, 6.12, and 252 µM, respectively). Fixed‐ratio combination experiments showed two distinct profiles: additivity for the uncompetitive + mixed pair (FC122 + UA) and competitive + competitive pairs (SUR + CGA), and antagonism for the competitive + uncompetitive combination (SUR + FC122). Docking and MD provided the structural basis for these results and suggested that each combination imposes a distinct structural flexibility profile on the disordered C‐terminal region of PTP1B (residues 300–400). For the first time, the MD‐AMBER‐Umbrella‐COM protocol was applied to generate a comparative membrane permeability profile for mechanistically diverse PTP1B inhibitors, proposing a permeability order (SUR > FC122 > CGA ≈ UA). These results suggest that kinetic compatibility is a more reliable predictor of promising inhibitor combinations than binding‐site geography alone, and they offer a rational framework for designing multisite PTP1B inhibition strategies in type 2 diabetes mellitus.